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Deoxyribonucleic acid (DNA) molecules carry the genetic code that determines many physical and functional characteristics of organisms. Each DNA molecule consists of two helical backbones or “strands.” The helical strands are bound to each other to form a double helix. Each DNA strand is made up of four types of nucleotide bases, namely, adenine, guanine, thiamine and cytosine. The nucleotide bases on one strand form geometrically specific bonds (hydrogen bonds) with nucleotide the same type on the adjacent strand. Thus, the bases bond in type-specific pairs, i.e., adenine to adenine, guanine to guanine, etc. If the strands are subsequently separated, each strand provides a pattern of successive bases that can be used as a template for reconstruction of a DNA molecule that is the same as the original DNA molecule. This process occurs naturally in living organisms and is known as “replication.”
Modern DNA analysis techniques are frequently used to identify, match or characterize DNA by determining the specific nucleotide sequence that exists in DNA sample. However, sometimes, the available DNA sample is relatively small—such as when the DNA originates from a microorganism or tiny drop of body fluid found at a crime scene. When the available DNA sample is small, it is necessary to amplify the DNA from the sample. This amplification is performed by a laboratory technique that, in many respects, mimics natural DNA replication. This laboratory technique is known as “polymerase chain reaction” (PCR). U.S. Pat. Nos. 4,683,202 and 4,683,195 describe basic PCR technology and the entire disclosures of both such patents are expressly incorporated herein by reference.
PCR is typically carried out in cycles, with each cycle consisting of three steps, namely denaturation, annealing and extension. Prior to the denaturation step, a sample mixture is typically prepared which contains the DNA (or a quantity of body fluid or tissue that is believed to contain the DNA), primers and enzyme(s).
During the denaturation step, all or substantially all (e.g., 99%) of the DNA double helix is separated into two individual complimentary strands. This has heretofore been done by heating a DNA sample mixture to a temperature of between about 90 and 105 degrees C. for a period of between about one and ten minutes. This elevated temperature causes thermal separation of the DNA double. In some applications, this increase in temperature can also serve to terminate chemical reactions which had begun within the sample during a previous cycle.
In the annealing step, the specific oligonucleotide primers are attached to the DNA strands. Primers are needed because the DNA enzymes cannot start DNA chains from scratch. Instead, the primer is required to determine the location along a particular DNA template at which the synthesis of the complementary strand will begin. This allows the technique to be used to amplify a particular target region of DNA by selection of primers that are specific to that target region. In essence, each primer is a synthetic segment of single-stranded DNA that contains about 20-30 bases and a chemical label which allows it to be located and identified. In most PCR procedures, two primers are used, one for each of the complementary single DNA strands produced during the denaturation step. The annealing step is typically accomplished by lowering the temperature to between about 50 and 60.degrees C. This causes the primers to attach to the individual DNA strands.
Once the annealing step has caused the primers to bind to the DNA strands, the temperature is again raised, typically to greater than 70 degrees C., causing the enzyme(s) to activate. This activation of the enzyme(s) causes replication of the DNA strands. More specifically, the enzyme(s) synthesizes new double-stranded DNA molecules by facilitating the joining of complementary nucleotides (i.e., the sugar joined to a base and to a phosphate group) in the sample mixture.
As a result, at the end of the first PCR cycle, two new DNA strands are present, each of which is identical to the original target DNA strand that was denatured and primed. Typically, about 30 of these thermal PCR cycles are required to provide a sufficient amount of DNA for analysis. This can be quite time consuming. For example, each thermal denaturation step can take about two minutes. Each annealing step can also take about two minutes. Then, each extension step can also take about two minutes. As a result, the thermal cycling in each PCR cycle may takes about six minutes and a full 30 cycle PCR amplification can take about 3 hours.
Moreover, in thermal PCR, if the temperatures and times of the cycles are not precisely controlled, the desired amplification may not be achieved. Furthermore, because thermal denaturing requires relatively high temperature, the enzyme(s) in the DNA sample mixture must be selected from a limited number of enzymes that remain stable at these elevated denaturation temperatures or, alternatively, additional enzyme must be added after each PCR cycle. In this regard, Taq polymerase is the enzyme frequently used in thermal PCR because it remains stable and does not break down at the DNA denaturation temperatures. However, high temperature enzymes such as Taq lack capabilities that may be available with other less temperature-stable enzymes. For example, Taq polymerase lacks a 3′ to 5′ exonuclease activity which, if present, allows the enzyme to identify misplaced bases and replace them with correct bases in the correct positions. The use of an enzyme that has 3′ to 5′ exonuclease activity can avoid potentially undesirable amplification of errors in the target sequence.
Also, thermal PCR is routinely limited to target sequences within a certain size range—e.g., between about 2000 and 3000 base pairs. The use of thermal PCR for amplification of larger targets (e.g., up to 50,000 base pairs) can require very long heating cycles and special enzymes that may not be stable in such long heating cycles.
PCR amplification has a wide range of clinical and investigational applications. For example, in subjects who are infected with a specific microorganism (e.g., a virus, bacterium, fungus, etc.), a sample of body fluid or tissue may contain such a small amount the infecting organism's DNA that direct identification of the organism's DNA is difficult or impossible. However, PCR can be used to amplify the infecting organism's DNA to provide an amount that can be easily analyzed and identified. For this reason, PCR is used in a number of diagnostic tests for infectious diseases. Additionally, in some instances, PCR techniques can be used to not only determine that a particular organism is present but to also quantify how much of the infecting organism is present in the fluid or tissue sample. Such quantification can be valuable in assessing the severity of the infection and/or the efficacy of an ongoing treatment (e.g., periodic measurement of viral load in individuals receiving antiviral therapy).
PCR is also used to facilitate testing and screening of donated blood for the presence of presence of even very low levels of infectious organisms (e.g., Hepatitis B virus (HBV); Hepatitis C virus (HCV 3.0); Human Immunodeficiency viruses Types 1 and 2 (HIV 1,2); Human T-Lymphotropic virus (HTLV-I/II); Syphilis (Treponema pallidum); West Nile virus (WNV) and Chagas disease (T. cruzi)
Moreover, PCR can be used in genetic counseling. For example, PCR techniques can be used to analyze small samples of a subject's blood for the presence or absence of certain genes (e.g., certain specific nucleic acid sequences), thereby indicating whether that subject is predisposed toward a particular disease or condition and/or predicting how that subject may respond to a particular drug or biologic treatment.
Additionally, PCR amplification has also been used to purify a DNA-containing sample or material. In such applications, PCR amplification is used to increase the amount of DNA in the sample or material until the proportional amount of the DNA in the sample or material far exceeds the amounts of contaminants, thus effectively reducing the proportional amounts of the contaminants to trivial levels.
Also, PCR amplification can also be used to create DNA libraries that are useable in conjunction with combinatorial chemistry techniques, for various clinical and investigational purposes.
In view of the wide range of potential applications for PCR amplification techniques and the inherent limitations and drawbacks associated with thermal PCR, the prior art has included various methods and devices which purportedly eliminate the need for thermal cycling during PCR or, at least, provide for faster thermal cycling to limit the time required for the process.
For example, United Kingdom Patent Application Publication No. GB2,247,880 (Stanley) describes non-thermal methods and apparatus for converting a double stranded nucleic acid to a denatured single stranded nucleic acid by applying an electric potential to a solution containing the nucleic acid. The described process may be carried out at ambient or near ambient temperature. The strand separation comes about by electron transfer to DNA that is free in the solution and adsorbed onto an electrode. In the examples provided, the solution containing the DNA also contains a mediator which receives electrons from the electrode and transfers them to the DNA to effect said strand separation. Such mediator is defined as “an inorganic or organic molecule which is capable of reversible electron transfer at an electrode and which passes electrons on to or receives electrons from a biological molecule, in this instance the nucleic acid present in solution.” It is further stated that the mediator “should be soluble in the solvent for the DNA (which may be water or a solvent other than water) and compounds having a redox potential of 0 to −2 volts, 25 preferably −0.2 to −1 volt and especially about −0.4 volts are preferred. Thus the mediator may be a water or solvent soluble compound having conjugated or aromatic groups and one or more hetero-atoms and may be a compound of the quinone or bipyridyl series, especially a viologen such as 5 methyl viologen or a salt thereof. The choice of mediator is not believed to be critical provided that its redox potential is within the required voltage range and compound does not otherwise affect or interfere with DNA or other materials present in 10 the solution such as enzymes or oligonucleotide probes. The use of a mediator enables the DNA or other nucleic acid material to be denatured into its individual strands at an applied voltage of −0.1 volt or less. Although denaturation has been observed by the present inventors at a voltage of −1 volt, it is believed that this may be an overvoltage and the voltage needed to bring about actual denaturation may be as low as −0.8 volts especially since the redox potential of the mediator is 20 typically 0.4 volts.” In some embodiments, the process may be carried out using a modified electrode “in which the electron transfer is e.g. by an electron donating or electron accepting compound such as a mediator coated onto, or adsorbed onto, the surface of the electrode which is otherwise of an inert material.” Or, “[t]he electron transfer may also be from or to an electrode consisting at least partially of a mediator compound e.g. formed wholly of the mediator compound.”
U.S. Pat. No. 6,365,400 (Stanley) describes a process for denaturing double-stranded nucleic acid material into its individual strands using an electrochemical cell. This process is an electrical treatment of the nucleic acid with a voltage applied to the nucleic acid material by an electrode. This process may be used in the detection of nucleic acid by hybridizing with a labeled probe or in the amplification of DNA by a polymerase chain reaction or ligase chain reaction. The process may also employ a promoter compound, such as methyl viologen, to speed denaturation.
PCT International Patent Publication WO9802573 (Purvis) also describes non-thermal methods and apparatus for converting a double stranded nucleic acid to a denatured single stranded nucleic acid by applying an electric potential to a solution containing the nucleic acid. An effective concentration of Lithium ions are added to the sample to act as a promoter of the denaturation.
United States Patent Application Publication No. 2011/0212492 (Hirahara) describes methods and devices wherein a PCR reaction solution is passed between electrodes and low voltage electrical current is passed through the reaction solution to generate sufficient Joule heat for the PCR cycle without electrolyzing the reaction solution. This method does use thermal cycling. The low voltage electrical current is merely used to precisely control the heating of the reaction solution.
Others have described the use of ultrasonic energy, rather than thermal cycling, in PCR. Specifically, United States Patent Application Publication No. 2008/002038 (Patno, et al.) describes a method and apparatus for processing a DNA or RNA sample within a sample processing module. The method includes the steps of providing a sample well within the sample processing module that contains the DNA or RNA sample, coupling ultrasonic energy from an external source into the sampling well and denaturing and fragmenting the DNA or RNA sample using the ultrasonic energy.
Also, microwave assistance has been described as a means for reducing the amount of thermal cycling required during a PCR process. Specifically, U.S. Pat. No. 7,537,917 describes a method of microwave assisted nucleic acid amplification by PCR in which at least the denaturing and extension steps are carried out under the influence of microwave radiation, while preventing the temperature of the sample from varying more than 40° C. from start to finish, and while maintaining the temperature of the sample from start to finish at no more than 60° C.
Additionally, United States Patent Application Publication No. 2003/0104466 (Knapp et al.) describes a non-thermal polymerase chain reaction method that is performed using a microfluidic device. The microfluidic device has a reaction chamber or channel that contains a target nucleic acid sequence and primer sequences, a source of a chemical denaturant and a source of polymerase enzyme fluidly connected to the reaction chamber or channel and a fluid direction system for delivering the chemical denaturant or the polymerase enzyme to the reaction chamber or channel. Complementary strands of the target nucleic acid sequence are “melted” by delivering a volume of the chemical denaturant to the reaction chamber or channel. The primer sequences are annealed to the target nucleic acid by eliminating a denaturing effect of the chemical denaturant. The primer sequences are then extended along the target nucleic acid sequence by delivering a volume of the polymerase enzyme to the reaction chamber or channel. These steps of melting, annealing and extending are repeated to amplify the target nucleic acid sequence.
The entire disclosure of each of the above-cited patents and published patent applications is expressly incorporated herein by reference.
There remains a need in the art for the development of further alternatives and improvements to the PCR and nucleic acid amplification techniques of the prior art to lessen the time required and/or the complexity of the process.